GlycoMiner: A new software tool to elucidate glycopeptide composition

Oliver Ozohanics, Judit Krenyacz, K. Ludányi, Ferenc Pollreisz, K. Vékey, L. Drahos

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment.

Original languageEnglish
Pages (from-to)3245-3254
Number of pages10
JournalRapid Communications in Mass Spectrometry
Volume22
Issue number20
DOIs
Publication statusPublished - Oct 30 2008

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Glycopeptides
Glycosylation
Chemical analysis
Liquid chromatography
Transferrin
Oligosaccharides
Mass spectrometry
Polysaccharides
Websites
Throughput
Ions
Peptides
Molecules

ASJC Scopus subject areas

  • Spectroscopy
  • Analytical Chemistry
  • Organic Chemistry

Cite this

GlycoMiner : A new software tool to elucidate glycopeptide composition. / Ozohanics, Oliver; Krenyacz, Judit; Ludányi, K.; Pollreisz, Ferenc; Vékey, K.; Drahos, L.

In: Rapid Communications in Mass Spectrometry, Vol. 22, No. 20, 30.10.2008, p. 3245-3254.

Research output: Contribution to journalArticle

Ozohanics, Oliver ; Krenyacz, Judit ; Ludányi, K. ; Pollreisz, Ferenc ; Vékey, K. ; Drahos, L. / GlycoMiner : A new software tool to elucidate glycopeptide composition. In: Rapid Communications in Mass Spectrometry. 2008 ; Vol. 22, No. 20. pp. 3245-3254.
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